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Gentoo's Bugzilla – Attachment 152479 Details for
Bug 127628
ebuild for Sali's modeller
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modeller-9.3.diff
modeller-9.3.diff (text/plain), 6.20 KB, created by
Justin Lecher (RETIRED)
on 2008-05-08 14:09:50 UTC
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Description:
modeller-9.3.diff
Filename:
MIME Type:
Creator:
Justin Lecher (RETIRED)
Created:
2008-05-08 14:09:50 UTC
Size:
6.20 KB
patch
obsolete
>--- /usr/portage/local/layman/science/sci-chemistry/modeller/modeller-9.3.ebuild 2008-04-11 08:04:35.000000000 +0200 >+++ /usr/portage/local/private-overlay-dev/sci-chemistry/modeller-bin/modeller-bin-9.3-r2.ebuild 2008-05-08 15:33:15.000000000 +0200 >@@ -2,25 +2,41 @@ > # Distributed under the terms of the GNU General Public License v2 > # $Header: $ > >-inherit eutils python >+inherit eutils python distutils > > MY_PV="${PV/./v}" >-LICENSE="modeller" >+MY_PN="${PN%-bin}" >+LICENSE="MODELLER" > KEYWORDS="~amd64 ~x86" >-DESCRIPTION="MODELLER is used for homology or comparative modeling of protein three-dimensional structures" >-SRC_URI="http://salilab.org/${PN}/${MY_PV}/${PN}-${MY_PV}.tar.gz" >-HOMEPAGE="http://salilab.org/${PN}/" >+DESCRIPTION="Protein structure modeling by satisfaction of spatial restraints" >+SRC_URI="http://salilab.org/${MY_PN}/${MY_PV}/${MY_PN}-${MY_PV}.tar.gz" >+HOMEPAGE="http://salilab.org/${MY_PN}/" > IUSE="" > RESTRICT="mirror" > SLOT="0" > >-RDEPEND=">=dev-lang/python-2.4" >+RDEPEND=">=dev-lang/python-2.4 >+ >=dev-lang/swig-1.3" > DEPEND="" > >+S="${WORKDIR}/${MY_PN}-${MY_PV}" >+ >+src_unpack(){ >+ unpack ${A} >+ epatch "${FILESDIR}"/${MY_PV}-setup.patch >+} >+ >+src_compile(){ >+ cd src/swig >+ swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i >+ distutils_src_compile >+} >+ > src_install(){ > python_version > >- VER=9v3 >+ IN_PATH=/opt/${MY_PN}${MY_PV} >+ > case ${ARCH} in > x86) EXECUTABLE_TYPE="i386-intel8";; > amd64) EXECUTABLE_TYPE="x86_64-intel8";; >@@ -28,75 +44,83 @@ > die "Unsupported Arch";; > esac > >- IN_PATH=/opt/modeller${VER} >- >- sed -e "s:EXECUTABLE_TYPE${VER}=xxx:EXECUTABLE_TYPE${VER}=${EXECUTABLE_TYPE}:g" \ >- -e "s:MODINSTALL${VER}=xxx:MODINSTALL${VER}=\"${IN_PATH}\":g" \ >- modeller-${VER}/bin/modscript > "${T}/mod${VER}" >+ sed -e "s:EXECUTABLE_TYPE${MY_PV}=xxx:EXECUTABLE_TYPE${MY_PV}=${EXECUTABLE_TYPE}:g" \ >+ -e "s:MODINSTALL${MY_PV}=xxx:MODINSTALL${MY_PV}=\"${IN_PATH}\":g" \ >+ bin/modscript > "${T}/mod${MY_PV}" > exeinto ${IN_PATH}/bin/ >- doexe "${T}/mod${VER}" >- dosym ${IN_PATH}/bin/mod${VER} /opt/bin/mod${VER} >+ doexe "${T}/mod${MY_PV}" >+ dosym ${IN_PATH}/bin/mod${MY_PV} /opt/bin/mod${MY_PV} > > sed -e "s;@TOPDIR\@;\"${IN_PATH}\";" \ >- -e "s;@EXETYPE\@;$EXECUTABLE_TYPE;" \ >- modeller-${VER}/bin/modpy.sh.in > "${T}/modpy.sh" >+ -e "s;@EXETYPE\@;$EXECUTABLE_TYPE;" \ >+ bin/modpy.sh.in > "${T}/modpy.sh" > doexe "${T}/modpy.sh" > >- insinto ${IN_PATH}/bin/ >- doins -r modeller-${VER}/bin/{*top,lib} >- exeinto ${IN_PATH}/bin/ >- doexe modeller-${VER}/bin/{modslave.py,mod${VER}_${EXECUTABLE_TYPE}} >+ insinto ${IN_PATH} >+ doins -r modlib > >- exeinto /usr/lib/python${PYVER}/site-packages/ >- doexe modeller-${VER}/lib/${EXECUTABLE_TYPE}/_modeller.so >- dosym ${IN_PATH}/modlib/modeller /usr/lib/python${PYVER}/site-packages/modeller >- dosym ${IN_PATH}/lib/${EXECUTABLE_TYPE}/_modeller.so\ >- /usr/lib/python${PYVER}/site-packages/_modeller.so >+ insinto ${IN_PATH}/bin >+ doins -r bin/{lib,*top} >+ exeinto ${IN_PATH}/bin >+ doexe bin/{modslave.py,mod${MY_PV}_${EXECUTABLE_TYPE}} > > exeinto ${IN_PATH}/lib/${EXECUTABLE_TYPE}/ >- doexe modeller-${VER}/lib/${EXECUTABLE_TYPE}/{lib*,_modeller.so} >- exeinto ${IN_PATH}/lib/${EXECUTABLE_TYPE}/python${PYVER}/ >- doexe modeller-${VER}/lib/${EXECUTABLE_TYPE}/python2.5/_modeller.so >- dosym ${IN_PATH}/lib/${EXECUTABLE_TYPE}/libmodeller.so.1 \ >- ${IN_PATH}/lib/${EXECUTABLE_TYPE}/libmodeller.so >- >- insinto ${IN_PATH}/modlib/ >- doins -r modeller-${VER}/modlib/{*mat,*lib,*prob,*mdt,*bin,*de,*inp,*ini,modeller} >- >- insinto ${IN_PATH}/ >- doins -r modeller-${VER}/src >+ doexe lib/${EXECUTABLE_TYPE}/lib* >+ dosym libmodeller.so.2 ${IN_PATH}/lib/${EXECUTABLE_TYPE}/libmodeller.so >+ doexe src/swig/build/lib.linux-$(uname -m)-${PYVER}/_modeller.so > >+ dodoc README INSTALLATION >+ dohtml doc/* > insinto /usr/share/${PN}/ >- doins -r modeller-${VER}/examples >- dohtml modeller-${VER}/doc/* >- dodoc modeller-${VER}/{README,ChangeLog} >- >- cat >> "${T}/config.py" <<- EOF >- install_dir = "${IN_PATH}/" >- license = "YOURLICENSEKEY" >- EOF >+ doins -r examples > >- insinto ${IN_PATH}/modlib/modeller/ >- doins "${T}/config.py" >+ dosym ${IN_PATH}/lib/${EXECUTABLE_TYPE}/_modeller.so \ >+ /usr/$(get_libdir)/python${PYVER}/site-packages/_modeller.so > } > >-pkg_postinst(){ >- #Adapted from BUG #127628 >- einfo "" >- einfo " If you need to define your own residues" >- einfo " read the FAQ and edit the following files:" >- einfo "" >- einfo " ${MY_D}/modlib/top_heav.lib" >- einfo " ${MY_D}/modlib/radii.lib" >- einfo " ${MY_D}/modlib/radii14.lib" >- einfo " ${MY_D}/modlib/restyp.lib" >- einfo "" >- einfo " Good Luck and Happy Modeling :D" >- einfo "" >- echo >- echo >- ewarn "Obtain a license Key from" >- ewarn "http://salilab.org/modeller/registration.html" >- ewarn "and change the appropriate line in" >- ewarn "${IN_PATH}/modlib/modeller/config.py" >+pkg_postinst() { >+ if [[ ! -e "${IN_PATH}/modlib/modeller/config.py" ]]; then >+ echo install_dir = '"'"${IN_PATH}/"'"'> ${IN_PATH}/modlib/modeller/config.py >+ fi >+ >+ if grep -q license ${IN_PATH}/modlib/modeller/config.py; then >+ einfo "A license key file is already present in ${IN_PATH}/modlib/modeller/config.py" >+ else >+ ewarn "Obtain a license Key from" >+ ewarn "http://salilab.org/modeller/registration.html" >+ ewarn "And run this before using modeller:" >+ ewarn "emerge --config =${CATEGORY}/${PF}" >+ ewarn "That way you can [re]enter your license key." >+ fi > } >+ >+pkg_postrm() { >+ ewarn "This package leaves a license Key file in ${IN_PATH}/modlib/modeller/config.py" >+ ewarn "that you need to remove to completely get rid of modeller." >+} >+ >+pkg_config() { >+ ewarn "Your license key is NOT checked for validity here." >+ ewarn " Make sure you type it in correctly." >+ eerror "If you CTRL+C out of this, modeller will not run!" >+ while true >+ do >+ einfo "Please enter your license key:" >+ read license_key1 >+ einfo "Please re-enter your license key:" >+ read license_key2 >+ if [[ "$license_key1" == "" ]] >+ then >+ echo "You entered a blank license key. Try again." >+ else >+ if [[ "$license_key1" == "$license_key2" ]] >+ then >+ echo license = '"'$license_key1'"' >> "${IN_PATH}/modlib/modeller/config.py" >+ einfo "Thank you!" >+ break >+ else >+ eerror "Your license key entries do not match. Try again." >+ fi >+ fi >+ done >+} >\ No newline at end of file
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bug 127628
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83152
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113953
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143526
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146038
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146043
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149811
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149813
| 152479